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Fu J, Hsiao T, Waffarn E, Meng W, Long KD, Frangaj K, Jones R, Gorur A, Shtewe A, Li M, Muntnich CB, Rogers K, Jiao W, Velasco M, Matsumoto R, Kubota M, Wells S, Danzl N, Ravella S, Iuga A, Vasilescu ER, Griesemer A, Weiner J, Farber DL, Luning Prak ET, Martinez M, Kato T, Hershberg U, Sykes M. Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.15.23298517. [PMID: 38014202 PMCID: PMC10680888 DOI: 10.1101/2023.11.15.23298517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
It is unknown how intestinal B cell populations and B cell receptor (BCR) repertoires are established and maintained over time in humans. Following intestinal transplantation (ITx), surveillance ileal mucosal biopsies provide a unique opportunity to map the dynamic establishment of gut lymphocyte populations. Using polychromatic flow cytometry that includes HLA allele group-specific mAbs distinguishing donor from recipient cells along with high throughput BCR sequencing, we tracked the establishment of recipient B cell populations and BCR repertoire in the allograft mucosa of ITx recipients. We confirm the early presence of naïve donor B cells in the circulation and, for the first time, document the establishment of recipient B cell populations, including B resident memory cells, in the intestinal allograft mucosa. Recipient B cell repopulation of the allograft was most rapid in infant (<1 year old)-derived allografts and, unlike T cell repopulation, did not correlate with rejection rates. While recipient memory B cell populations were increased in graft mucosa compared to circulation, naïve recipient B cells remained detectable in the graft mucosa for years. Comparisons of peripheral and intra-mucosal B cell repertoires in the absence of rejection revealed increased BCR mutation rates and clonal expansion in graft mucosa compared to circulating B cells, but these parameters did not increase markedly after the first year post-transplant. Furthermore, clonal mixing between the allograft mucosa and the circulation was significantly greater in ITx recipients, even years after transplantation, than in healthy control adults. Collectively, our data demonstrate intestinal mucosal B cell repertoire establishment from a circulating pool, a process that continues for years without evidence of establishment of a stable mucosal B cell repertoire.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Thomas Hsiao
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Elizabeth Waffarn
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine D Long
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kristjana Frangaj
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rebecca Jones
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Alaka Gorur
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Areen Shtewe
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Muyang Li
- Department of Pathology, Columbia University, New York, NY, USA
| | - Constanza Bay Muntnich
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kortney Rogers
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenyu Jiao
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Monica Velasco
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rei Matsumoto
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Masaru Kubota
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Steven Wells
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nichole Danzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shilpa Ravella
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Alina Iuga
- Department of Pathology, Columbia University, New York, NY, USA
| | | | - Adam Griesemer
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Joshua Weiner
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Tomoaki Kato
- Department of Surgery, Columbia University, New York, NY, USA
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
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Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB. TooManyCells identifies and visualizes relationships of single-cell clades. Nat Methods 2020; 17:405-413. [PMID: 32123397 PMCID: PMC7439807 DOI: 10.1038/s41592-020-0748-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/15/2020] [Indexed: 01/24/2023]
Abstract
Identifying and visualizing transcriptionally similar cells is instrumental for accurate exploration of the cellular diversity revealed by single-cell transcriptomics. However, widely used clustering and visualization algorithms produce a fixed number of cell clusters. A fixed clustering 'resolution' hampers our ability to identify and visualize echelons of cell states. We developed TooManyCells, a suite of graph-based algorithms for efficient and unbiased identification and visualization of cell clades. TooManyCells introduces a visualization model built on a concept intentionally orthogonal to dimensionality-reduction methods. TooManyCells is also equipped with an efficient matrix-free divisive hierarchical spectral clustering different from prevalent single-resolution clustering methods. TooManyCells enables multiresolution and multifaceted exploration of single-cell clades. An advantage of this paradigm is the immediate detection of rare and common populations that outperforms popular clustering and visualization algorithms, as demonstrated using existing single-cell transcriptomic data sets and new data modeling drug-resistance acquisition in leukemic T cells.
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Affiliation(s)
- Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Fasolino
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M Shaffer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Schwartz GW, Petrovic J, Zhou Y, Faryabi RB. Differential Integration of Transcriptome and Proteome Identifies Pan-Cancer Prognostic Biomarkers. Front Genet 2018; 9:205. [PMID: 29971090 PMCID: PMC6018483 DOI: 10.3389/fgene.2018.00205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
High-throughput analysis of the transcriptome and proteome individually are used to interrogate complex oncogenic processes in cancer. However, an outstanding challenge is how to combine these complementary, yet partially disparate data sources to accurately identify tumor-specific gene products and clinical biomarkers. Here, we introduce inteGREAT for robust and scalable differential integration of high-throughput measurements. With inteGREAT, each data source is represented as a co-expression network, which is analyzed to characterize the local and global structure of each node across networks. inteGREAT scores the degree by which the topology of each gene in both transcriptome and proteome networks are conserved within a tumor type, yet different from other normal or malignant cells. We demonstrated the high performance of inteGREAT based on several analyses: deconvolving synthetic networks, rediscovering known diagnostic biomarkers, establishing relationships between tumor lineages, and elucidating putative prognostic biomarkers which we experimentally validated. Furthermore, we introduce the application of a clumpiness measure to quantitatively describe tumor lineage similarity. Together, inteGREAT not only infers functional and clinical insights from the integration of transcriptomic and proteomic data sources in cancer, but also can be readily applied to other heterogeneous high-throughput data sources. inteGREAT is open source and available to download from https://github.com/faryabib/inteGREAT.
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Affiliation(s)
- Gregory W. Schwartz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Robert B. Faryabi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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Meng W, Zhang B, Schwartz GW, Rosenfeld AM, Ren D, Thome JJ, Carpenter DJ, Matsuoka N, Lerner H, Friedman AL, Granot T, Farber DL, Shlomchik MJ, Hershberg U, Luning Prak ET. An atlas of B-cell clonal distribution in the human body. Nat Biotechnol 2017; 35:879-884. [PMID: 28829438 PMCID: PMC5679700 DOI: 10.1038/nbt.3942] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
Abstract
B-cell responses result in clonal expansion, and can occur in a variety of tissues. To define how B-cell clones are distributed in the body, we sequenced 933,427 B-cell clonal lineages and mapped them to eight different anatomic compartments in six human organ donors. We show that large B-cell clones partition into two broad networks-one spans the blood, bone marrow, spleen and lung, while the other is restricted to tissues within the gastrointestinal (GI) tract (jejunum, ileum and colon). Notably, GI tract clones display extensive sharing of sequence variants among different portions of the tract and have higher frequencies of somatic hypermutation, suggesting extensive and serial rounds of clonal expansion and selection. Our findings provide an anatomic atlas of B-cell clonal lineages, their properties and tissue connections. This resource serves as a foundation for studies of tissue-based immunity, including vaccine responses, infections, autoimmunity and cancer.
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Affiliation(s)
- Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bochao Zhang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
| | - Gregory W. Schwartz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Aaron M. Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
| | - Daqiu Ren
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Joseph J.C. Thome
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY
| | - Dustin J. Carpenter
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY
| | - Nobuhide Matsuoka
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY
| | | | | | - Tomer Granot
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY
| | - Donna L. Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY
- Department of Surgery and Department of Microbiology and Immunology, Columbia University School of Medicine, New York, NY
| | | | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA
- Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, PA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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